Bioinformatics CentreBioinformatics Centre- A Profile- A Profile

Commissioning of the Centre 1992-93

Phone : +91 413 2655212 Fax : +91 413 2655211/265

E-mail : bicpu2001@yahoo.co.in

University webpage: http://www.pondiuni.org/bioinformatics.htmlCentre website: http://bicpu.edu.in

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About UniversityAbout University

Pondicherry University is a Central University established by an Act of Parliament No. 53 of 1985 fully supported by the University Grants Commission.

Pondicherry University was the first to provide the students with the Choice Based Credit System (CBCS)

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School of Life SciencesSchool of Life Sciences

The University is organized at several levels for efficient functioning (Schools/Departments/Centres).

The School of Life Sciences comprises the following Departments / Centres viz., Department of Biochemistry & Molecular Biology, Department of Biotechnology, Department of Ecology and Environmental Science, Department of Ocean Studies & Marine Biology, Centre for Pollution Control & Energy Technology and Bioinformatics Centre.

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Bioinformatics CentreBioinformatics Centre

1991-1992 Centre was established as Sub-Distributed Information Centre (Sub-DIC) with support of DBT

1995 Service provider with facilities for sequence retrieval and analysis and abstract services

2001 Started one year Advanced Post Graduate Diploma course in Bioinformatics

2004 Sub-DIC was upgraded as a full-fledged center with DIC Status

2005 Started Molecular Modeling facility (Silicon Graphics System with Insight-II & DS Modeling server) and Linux based Beowulf type Clustering

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PersonnelPersonnel TeachingTeaching

Coordinator Prof. P.P. MathurReader 1 No. (Vacant)Lecturer Dr. D. Sundar Lecturer 1 No. (Vacant)Temporary Faculties 3 Nos.

TechnicalTechnicalInformation Officer Mr. M. Sundara Mohan Technical Assistant Ms. V. AmoudaComputer Operator Mr. E. Selvakumar Computer Operator Ms. N. ShanthiData Entry Operator 1 No. (Vacant)

OfficeOfficeAttendant Mr. T. Gopy

Temporary positionsTemporary positions DBT-JRF 1 No. (Vacant) DBT-Traineeship 2 Nos. (Vacant) DBT-Studentship 2 Nos. (Vacant)

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ActivitiesActivities TeachingTeaching

Regular M.Sc Program in Bioinformatics (applied to UGC)

Advanced PG Diploma in Bioinformatics (since 2001)

TrainingTraining Regular Training Programs (Short term & Long term)

ResearchResearch Molecular Dynamics simulation of Human Transferrin Protein Engineering of DNA-binding Proteins Database and Software Development

ExtensionExtension Development of E-Learning modules in Bioinformatics

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Teaching ProgramTeaching Programo The Centre has been offering an Advanced Post Graduate

Diploma Course in Bioinformatics since the Academic year 2001-2002 with the support from Department of Biotechnology, New Delhi

o The students are selected through a competitive examination conducted at the All India Level in 14 Centres in the month of June followed by a personal interview

o Only those candidates who have Master’s degree in any branch of Biological Sciences, Molecular Biology/ Biotechnology/ Biochemistry/ Biophysics/ Microbiology/ M.B.B.S/ Life Sciences/ Botany/ Zoology are currently eligible to join the Advanced PG Diploma program in Bioinformatics.

o A sum of Rs. 5000/- per month is offered as a stipend to the selected students.

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Students PlacementsStudents Placementso Johns Hopkins University, Baltimore, USA

o HCL Technologies Limited

o Institute of Bioinformatics, Bangalore

o Protein Lounge, Orissa

o Central Sericulture Research & Training Institute, Mysore

o Vector Control Research Centre, Pondicherry

o Orissa Agricultural University, Orissa

o HNB Garhwal University, Srinagar

o University of Madras, Chennai

o Pondicherry University, Pondicherry

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Training ProgramTraining Programo Training Programs (Short term)Training Programs (Short term)

The Bioinformatics Centre regular short term training program every year during Jan-Feb. We have so far conducted 18 National Level Seminars / Workshops / Training Programs since 1991.

o Training Programs (Long term)Training Programs (Long term)

The Centre accepts students who have qualified the DBT-Junior Research Fellowship All India Examination for the Ph.D. program in Bioinformatics.

DBT has sanctioned two positions each for Traineeship and Studentship in Bioinformatics every year. The students selected under these two schemes will be awarded a stipend of Rs. 5000 per month.

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Forthcoming SeminarsForthcoming Seminars

National Seminar on "Intellectual Property Rights in Bioinformatics & Biotechnology" to be organized by our Centre during September 15-16, 2005.

National Seminar on "Advances in Nanosciences and Nanobiotechnology" to be organized by our Centre during December 05-06, 2005.

National Seminar on "Bioinformatics and Functional Genomics" to be organized by our Centre during February 15-17, 2006.

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InfrastructureInfrastructure- Hardware- Hardware

ServersServersWipro Processor: Xeon@3.0 Ghz; RAM: 1 GB; HDD: 120

GB; OS:Red Hat Linux 9;  12/24GB-DAT drive1

HCL (AMD Opteron 64 BIT)

Processor: AMD 8131/8111 Motherboard (Dual Processor Capable); RAM: 1 GB; HDD: 100 GB; OS:Windows 2003 Server;    12/24GB-DAT drive;

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HP-Vectra Processor: Pentium III@833 Mhz; RAM:128 MB; HDD:30 GB; OS: Red Hat Linux 9

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Specialized WorkstationsSpecialized WorkstationsSilicon Graphics (Onyx3 Fuel)

Processor: 800Mhz. MIPS R16000 (IP35) with MIPS R16000 FPU; RAM: 1 GB;  HDD:176 GB; OS: IRIX64 Release 6.5; Graphics: V10)

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DSM Modeling Server

Processor: Pentium IV@2.8 Ghz.; RAM: 512+256; HDD:40 GB; OS:Windows XP; CD-RW; DVD-RW

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Workstation Cluster Beowulf type Cluster (Linux based) 1 Master + 5 Slaves

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InfrastructureInfrastructure- Hardware- Hardware

WorkstationsWorkstations

25 Workstations Intel Pentium IV with Dual Operating Systems (Red Hat Linux 9 & Windows XP Professional). All workstations are connected with a domain name server on Windows 2003 server.

PrintersPrinters

HP 4600 DN Color Laser, HP 2200DN Laser printer, HP 1150 Laser Printer, HP 4P-Laser printer, HP Inkjet 5748, 810 & 670 C

AccessoriesAccessories

Sony DVD Writer, HP CD-Writer, HP Scanner, Modem, Infocus LCD Projector, Kodak Digital Camera, Sony Internal Cd-Writers, Web Camera, Toshiba Multifunctional Copier, Toshiba Multifunctional Fax and Hitachi Hi-Fax, Uninterrupted power supply (10 KVA – 1 no. & 5.0 KVA- 2 nos., 0.6 KVA UPS – 4 nos.)

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InfrastructureInfrastructure- Software- Software

Academic LicensedAcademic LicensedAmber - Molecular Dynamics simulationAutoDock - Molecular Docking (Flexible Ligand docking)Dock - Molecular Docking (Rigid docking)GROMOS96 - Molecular Dynamics simulationModeller - Homology ModelingPhred, Phrap, Consed - Sequence AnalysisWhatif - Protein Structure Modeling & validation suite

Vendors LicensedVendors LicensedInsight II 2005 (single user with 5 years term license)Affinity, Discover Bundle, Biopolymer, Homology, Ludi

DS Modeling Suite 1.5 (single user with 5 years term license)Visualizer, Project KM plus, Analysis, Biopolymer, CHARMm, Delphi, LigandFit, Ligand Score, Ludi, Modeler, MS Search, Protein Families, Protein Health, Protein Similarity Search

Trends Micro's Enterprise Solution (Neat Suite)EndnoteStatistica

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InfrastructureInfrastructure- Software- Software

Academic free & Open Source suitesAcademic free & Open Source suites

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InfrastructureInfrastructure- Communication- Communication

InternetInternetA 4 Mbps (Megabit per second) leased circuit Radio Link Internet connectivity from the Software Technology Parks of India (STPI), Pondicherry provides round the clock internet access.

The computing facilities in the Bioinformatics Centre are available to the students round the clock on 24 hours/day, 365 days/year basis.

IntranetIntranetAll the buildings in the Campus are interconnected through a Fiber Optic backbone with CISCO switches and routers. The connectivity to workstations is using UTP Cable ensuring a dedicated 100 Mbps bandwidth at desktop level.

The intranet acts as a platform for Internet, UGC-Infonet, Library services and University automation functions

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Bioinformatics Centre LibraryBioinformatics Centre Library The INFLIBNET Centre, Ahmedabad is providing access to

the scholarly e-journals under UGC-Infonet E-Journals Consortium. As part of the consortium, access to the Electronic databases/ Journals of the Science Direct is also provided through the campus-wide Intranet to our Bioinformatics Centre.

The Central Library of Pondicherry University has a collection of over 96821 books and several scientific journals.

The Bioinformatics Centre subscribes to several important Journals like Bioinformatics, Journal of Bioinformatics and Computational Biology (JBCB), Briefings in Bioinformatics, Nature, Nature Structural Biology, Science, Scientific American, Linux for You for its departmental library. The Bioinformatics Centre library holdings include Books (300) and Journals (8).

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Bioinformatics Centre e-LibraryBioinformatics Centre e-Library

Collaborating DepartmentCollaborating Department

The Centre has a close collaboration with the Department of Biochemistry & Molecular Biology within the School of Life Sciences.

This Department is recognized for special funding under DST-FIST program and has also attracted extramural funding worth several lakhs.

The Departmental Faculty has established research collaborations with foreign investigators as well as with the Bioinformatics Centre in teaching and wet-lab research.

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InfrastructureInfrastructure- Wet Lab- Wet Lab

UV-Visible Spectrophotometer

Shimadzu UV-1700Pharmaspec

High Speed Centrifuge Hitachi Himach CR 26H

Sorvall RC 5C Plus

Ultracentrifuge Sorvall RC 90

Gel Documentation System Syngene Ingenius

Gamma Counter LKB Wallac 1275 Mini Gamma

Liquid Scintilation Counter LKB Wallac 1209 Rack Beta

ELISA Reader Multiscope

Laminar Flow Chamber Yorco

Homogenizer Polytron PT 3000

CO2 Incubator VWR scientific Model 2100

Thermo Forma Model 311

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Phase Contrast Microscope Leica DM IL

Lynx Vision 2000

PCR Eppendorf

Deep Freezer -80°C Sanyo MDF U6086SUltrasonication (Sonifier) Branson 450DMicrofuge Fisher Model 235ANitrogen Analyzer Kjel Plus Distil –MMetabolic Shaker Incubator Orbitek

Gel Electrophoresis BioRad / Hoefer

Fraction Collector Bio Rad / Hoefer

InfrastructureInfrastructure- Wet Lab- Wet Lab

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Research CollaborationsResearch Collaborations Johns Hopkins University, Baltimore, USAJohns Hopkins University, Baltimore, USA

Protein engineering of DNA recognition motifs, artificial ZF-transcription factors/repressors and in particular Zinc Finger Nucleases (ZFNs) to target and achieve highly efficient and permanent genome modification of plants and mammals including the humans.

Anna University – ChennaiAnna University – ChennaiMolecular Modeling & High Performance / Cluster Computing

Central Leather Research Institute – ChennaiCentral Leather Research Institute – ChennaiMolecular Dynamics Simulations

Kern Labs Private Limited, ChennaiKern Labs Private Limited, ChennaiDevelopment of e-learning modules in Bioinformatics

Possible collaboration with Possible collaboration with Ecole Superieure De Physique Ecole Superieure De Physique et Chimie Industrielles, Paris, Franceet Chimie Industrielles, Paris, FranceProf. Brigitte Quenet Neural Networking (Formal modeling with multistate neurones and multidimensional synapses)

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Research CollaborationsResearch Collaborations

Biogrid IndiaBiogrid India

Our centre will be soon connected to Biogrid (a Virtual Private Network of the Department of Biotechnology, Govt. of India) enabling access by student and scientific community from across the country. It is envisioned that the Biogrid will span all the 60+ Bioinformatics centres of the Department of Biotechnology with Gbps bandwidth and 10+ Teraflops of computational power..

Research FocusResearch Focus

Database & Software DevelopmentDatabase & Software Development EST & SNP database Analytical tools for Genome analysis

Molecular Modeling studiesMolecular Modeling studies Molecular Dynamics simulation of human serum

Transferrin as a heavy metal transporter – an approach for targeted drug delivery

Protein Engineering of DNA-binding ProteinsProtein Engineering of DNA-binding Proteins

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Research Publications (2004)Research Publications (2004)Swarnalatha, M., Jutur, P.P., Amouda, V., Mathur, P.P., A.R. Reddy (2004) Prediction of Transcriptional Regulation by Dlx and Msx homeodomain proteins. Online J. Bioinformatics 5: 132-145.

Mathur, P.P. (2004) Bioinformatics: From Pre-Genomic to Post-Genomic Era, Advanced Biotech. 3:27-31.

Kumaran, K. and Mathur, P.P. (2004). Computational analysis reveals potential vaccine candidates for SARS Coronavirus, Asia Pacific Bioinformatics Conference conducted by the Institute of Infocomm Research, Singapore, January 2005.

Sundar D, A.D. Bosley, A.B. Abulencia, S. Chandrasegaran and M. Ostermeier (2004). A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. FASEB Journal 18(8): C174.

Kandavelou, K., M. Mani, Sundar D. and S. Chandrasegaran (2004). Engineering and applications of chimeric nucleases. In: Nucleic Acids & Molecular Biology, Vol. 14, A. M. Pingoud (Ed.). Restriction Endonucleases, pp. 413-434, Springer-Verlag, Berlin, Heidelberg, Germany.

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Mani, M., K. Kandavelou, Sundar D. and S. Chandrasegaran (2005). Design, engineering and characterization of zinc finger nucleases for gene targeting. Biochemical & Biophysical Research Communications 335: 447-457.

Sundar D., A.D. Bosley, A.B. Abulencia, S. Chandrasegaran and M. Ostermeier (2005). A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. Combinatorial Chemistry & High Throughput Screening (in press).

Kandavelou, K., M. Mani, Sundar D. and S. Chandrasegaran (2005). “Magic” scissors for genome surgery. Nature Biotechnology 23(6): 686-687.

Sundar D., Kandavelou, K., M. Mani, M. Porteus and S. Chandrasegaran (2005). Zinc finger nucleases: custom-designed molecular scissors. Nucleic Acids Research (Invited article, submitted)

Amouda, V. Shanthi, N. and Palanivelu. K (2005) Aspect-Oriented Programming: A new approach for biological database, Advances in Bioinformatics and Computational Biology (submitted).

Arul Prakasam, P., Lakshminarayanan, S., Selvakumar, E. and Mathur, P.P. (2005). Three Dimensional Structure of Human 15-Lipoxygenase predicted by homology-based modeling - a potential target for atherosclerosis and cancer. Journal of Molecular Modeling (submitted).

Balamurugan. R, Selvakumar, E. and Mathur, P.P. (2005) Molecular Dynamics Simulation of Human Serum Transferrin as a heavy metal transporter - An approach for targeted drug delivery. Journal of Molecular Modeling (submitted).

Research Publications (2005)Research Publications (2005)

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For more details please visit… For more details please visit… http://www.bicpu.edu.in

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Bioinformatics Centre, Pondicherry UniversityBioinformatics Centre, Pondicherry University